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1. Full Text A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
by Zang, Chongzhi and Schones, Dustin E and Zeng, Chen and Cui, Kairong and Zhao, Keji and Peng, Weiqun
Bioinformatics, ISSN 1367-4803, 8/2009, Volume 25, Issue 15, pp. 1952 - 1958
Motivation: Chromatin states are the key to gene regulation and cell identity. Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing... 
FALSE DISCOVERY RATE | TRANSCRIPTION FACTOR-BINDING | RECOGNITION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | EMBRYONIC STEM-CELLS | METHYLATIONS | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SITES | LYSINE 9 | PROTEINS | GENOME-WIDE IDENTIFICATION | Protein Structure, Tertiary | Computational Biology - methods | Chromatin Immunoprecipitation | Histones - chemistry | Genome | Sequence Analysis, DNA | Cluster Analysis | Index Medicus | Original Papers
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2. Full Text H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions
by Wei, Gang and Zhao, Keji and Jin, Chunyuan and Peng, Weiqun and Felsenfeld, Gary and Cui, Kairong and Zang, Chongzhi
Nature Genetics, ISSN 1061-4036, 08/2009, Volume 41, Issue 8, pp. 941 - 945
To understand how chromatin structure is organized by different histone variants, we have measured the genome-wide distribution of nucleosome core particles... 
H3.3 | CHROMATIN | HUMAN-CELLS | GENETICS & HEREDITY | GENE-EXPRESSION | GENOME-WIDE | HISTONE MODIFICATIONS | IDENTIFICATION | SACCHAROMYCES-CEREVISIAE | H2A.Z | OCCUPANCY | Protein Isoforms - metabolism | Humans | Transcription Initiation Site | Nucleosomes - metabolism | Transcription, Genetic | HeLa Cells | Histones - metabolism | Promoter Regions, Genetic - genetics | Physiological aspects | Nucleosomes | Chromatin | Promoters (Genetics) | Research | Structure | Studies | Proteins | Kidney diseases | Gene expression | Methods | Binding sites | Index Medicus
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3. Full Text Partitioning heritability by functional annotation using genome-wide association summary statistics
by Finucane, Hilary K and Bulik-Sullivan, Brendan and Gusev, Alexander and Trynka, Gosia and Reshef, Yakir and Loh, Po-Ru and Anttila, Verneri and Xu, Han and Zang, Chongzhi and Farh, Kyle and Ripke, Stephan and Day, Felix R and Purcell, Shaun and Stahl, Eli and Lindstrom, Sara and Perry, John R.B and Okada, Yukinori and Raychaudhuri, Soumya and Daly, Mark J and Patterson, Nick and Neale, Benjamin M and Price, Alkes L and RACI Consortium and Psychiat Genomics Consortium and ReproGen Consortium and The RACI Consortium and Schizophrenia Working Group of the Psychiatric Genomics Consortium
Nature Genetics, ISSN 1061-4036, 11/2015, Volume 47, Issue 11, pp. 1228 - 1235
Recent work has demonstrated that some functional categories of the genome contribute disproportionately to the heritability of complex diseases. Here we... 
HUMAN HEIGHT | VARIANTS | COMMON SNPS | DISEASE | SUSCEPTIBILITY | GENETICS & HEREDITY | BODY-MASS INDEX | GENETIC ARCHITECTURE | LOCI | PROPORTION | CELL-TYPES | Genome-wide association studies | Genetic research | Heritability | Genetic aspects | Research | Population genetics | Methods | Studies | Economic models | Statistics | Index Medicus
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4. Full Text Combinatorial patterns of histone acetylations and methylations in the human genome
by Wang, Zhibin and Zhang, Michael Q and Zhao, Keji and Roh, Tae-Young and Peng, Weiqun and Rosenfeld, Jeffrey A and Cuddapah, Suresh and Schones, Dustin E and Barski, Artem and Zang, Chongzhi and Cui, Kairong
Nature Genetics, ISSN 1061-4036, 07/2008, Volume 40, Issue 7, pp. 897 - 903
Histones are characterized by numerous posttranslational modifications that influence gene transcription. However, because of the lack of global distribution... 
LANGUAGE | COMPLEX | CODE | CHROMATIN DOMAINS | TRANSCRIPTION | GENETICS & HEREDITY | GENE-EXPRESSION | ENHANCERS | T-CELLS | Protein Methyltransferases | Promoter Regions, Genetic | Humans | Cells, Cultured | Chromosome Mapping | Genome, Human - physiology | Enhancer Elements, Genetic | Histone-Lysine N-Methyltransferase - metabolism | Histone Acetyltransferases - metabolism | Protein Binding | Acetylation | Histones - metabolism | Methylation | Cluster Analysis | Histones | Research | Genetic transcription | DNA damage | Proteins | Chromatin | Genomics | Index Medicus
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5. Full Text Target analysis by integration of transcriptome and ChIP-seq data with BETA
by Wang, Su and Sun, Hanfei and Ma, Jian and Zang, Chongzhi and Wang, Chenfei and Wang, Juan and Tang, Qianzi and Meyer, Clifford A and Zhang, Yong and Liu, X. Shirley
Nature Protocols, ISSN 1754-2189, 2013, Volume 8, Issue 12, pp. 2502 - 2515
The combination of ChIP-seq and transcriptome analysis is a compelling approach to unravel the regulation of gene expression. Several recently published... 
GENE-EXPRESSION | ELEMENT | IDENTIFICATION | BIOCHEMICAL RESEARCH METHODS | GENOME BROWSER | PREDICTION | Chromatin Immunoprecipitation - methods | Gene Expression Profiling - methods | Software | Transcriptome | Gene targeting | Equipment and supplies | Gene expression | Observations | Properties | Genetic screening | Methods | Binding sites (Biochemistry) | Index Medicus
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6. Full Text Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
by He, Housheng Hansen and Meyer, Clifford A and Hu, Sheng'En Shawn and Chen, Mei-Wei and Zang, Chongzhi and Liu, Yin and Rao, Prakash K and Fei, Teng and Xu, Han and Long, Henry and Liu, X. Shirley and Brown, Myles
Nature Methods, ISSN 1548-7091, 2014, Volume 11, Issue 1, pp. 73 - 78
Sequencing of DNase I hypersensitive sites (DNase-seq) is a powerful technique for identifying cis-regulatory elements across the genome. We studied the key... 
Transcription Factors - chemistry | Nucleosomes - chemistry | Humans | Gene Expression Regulation | Male | Gene Regulatory Networks | Amino Acid Motifs | Nucleotides - chemistry | Deoxyribonuclease I - chemistry | MCF-7 Cells | K562 Cells | Cell Line, Tumor | Female | Receptors, Androgen - chemistry | Tumor Suppressor Protein p53 - chemistry | Binding Sites | Sequence Analysis, DNA - methods | Chromatin - chemistry | Transcription factors | Dornase alfa | Physiological aspects | Genetic aspects | DNA testing | Research | Methods | Proteins | Chromatin | Genomics | Deoxyribonucleic acid--DNA | Index Medicus
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7. Full Text Global Mapping of H3K4me3 and H3K27me3 Reveals Specificity and Plasticity in Lineage Fate Determination of Differentiating CD4 + T Cells
by Wei, Gang and Wei, Lai and Zhu, Jinfang and Zang, Chongzhi and Hu-Li, Jane and Yao, Zhengju and Cui, Kairong and Kanno, Yuka and Roh, Tae-Young and Watford, Wendy T and Schones, Dustin E and Peng, Weiqun and Sun, Hong-wei and Paul, William E and O'Shea, John J and Zhao, Keji
Immunity, ISSN 1074-7613, 2009, Volume 30, Issue 1, pp. 155 - 167
Multipotential naive CD4 T cells differentiate into distinct lineages including T helper 1 (Th1), Th2, Th17, and inducible T regulatory (iTreg) cells. The... 
SYSBIO | MOLIMMUNO | TRANSCRIPTION FACTORS | HELPER TYPE-1 | FOXP3 EXPRESSION | HUMAN GENOME | TGF-BETA | T(H)17 CELLS | TH2 CELLS | EMBRYONIC STEM-CELLS | GENE-EXPRESSION | IMMUNOLOGY | TH17 CELLS | T-Lymphocyte Subsets - immunology | Oxidoreductases, N-Demethylating - genetics | Mice, Inbred C57BL | Chromosome Mapping | Protein Modification, Translational | CD4-Positive T-Lymphocytes - immunology | Oxidoreductases, N-Demethylating - immunology | Animals | Mice | Retinoblastoma-Binding Protein 2 | Histones - metabolism | Jumonji Domain-Containing Histone Demethylases | Cell Lineage - genetics | CD4 Antigens - metabolism | Cell Lineage - immunology | DNA-Binding Proteins | Epigenetics | Transcription factors | Cytokines | Gene expression | Stem cells | Index Medicus
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8. Full Text Discrete Roles of STAT4 and STAT6 Transcription Factors in Tuning Epigenetic Modifications and Transcription during T Helper Cell Differentiation
by Wei, Lai and Vahedi, Golnaz and Sun, Hong-Wei and Watford, Wendy T and Takatori, Hiroaki and Ramos, Haydee L and Takahashi, Hayato and Liang, Jonathan and Gutierrez-Cruz, Gustavo and Zang, Chongzhi and Peng, Weiqun and O'Shea, John J and Kanno, Yuka
Immunity, ISSN 1074-7613, 2010, Volume 32, Issue 6, pp. 840 - 851
Signal transducer and activator of transcription 4 (STAT4) and STAT6 are key factors in the specification of helper T cells; however, their direct roles in... 
SYSBIO | MOLIMMUNO | CHIP-SEQ DATA | TARGET GENES | DNA-BINDING | INTERFERON-GAMMA | FACTOR GATA-3 | FATE DETERMINATION | IMMUNOLOGY | HISTONE MODIFICATIONS | BINDING-SITES | GENOME-WIDE IDENTIFICATION | EXPRESSION | Gene Expression | T-Lymphocytes, Helper-Inducer - metabolism | Oligonucleotide Array Sequence Analysis | Gene Expression Regulation - immunology | Epigenesis, Genetic | Mice, Inbred C57BL | STAT6 Transcription Factor - genetics | STAT6 Transcription Factor - immunology | Mice, Knockout | Cell Differentiation - immunology | Animals | Chromatin Immunoprecipitation | T-Lymphocytes, Helper-Inducer - immunology | T-Lymphocytes, Helper-Inducer - cytology | STAT4 Transcription Factor - genetics | Transcription, Genetic | Mice | STAT4 Transcription Factor - immunology | Medical law | Chromatin | Anopheles | DNA binding proteins | T cells | Stem cells | Data analysis | Transcription factors | Cytokines | Genomics | Epigenetics | Software | Genomes | Gene expression | Recruitment | Index Medicus
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9. Full Text NOTCH1—RBPJ complexes drive target gene expression through dynamic interactions with superenhancers
by Hongfang Wang and Chongzhi Zang and Len Taing and Kelly L. Arnett and Yinling Joey Wong and Warren S. Pear and Stephen C. Blacklow and Shirley Liu and Jon C. Aster
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 1/2014, Volume 111, Issue 2, pp. 705 - 710
The main oncogenic driver in T-lymphoblastic leukemia is NOTCH1, which activates genes by forming chromatin-associated Notch transcription complexes.... 
T lymphocytes | Chromatin | Genes | Genomics | Leukemia | Cell lines | Genomes | Gene expression | Genetic mutation | Binding sites | TRANSCRIPTION FACTORS | ACTIVATION | MULTIDISCIPLINARY SCIENCES | CELL IDENTITY | GENOME | SUPER-ENHANCERS | gene regulation | Notch signaling | DISEASE | MUTATIONS | DOMAINS | BINDING | LYMPHOBLASTIC-LEUKEMIA | Immunoglobulin J Recombination Signal Sequence-Binding Protein - metabolism | Receptors, Interleukin-7 - metabolism | Gene Expression Regulation - genetics | Humans | Gene Expression Regulation - physiology | DNA Primers - genetics | Signal Transduction - genetics | Binding Sites - genetics | Receptor, Notch1 - metabolism | Promoter Regions, Genetic - genetics | Multiprotein Complexes - metabolism | Chromatin Immunoprecipitation | Luciferases | Plasmids - genetics | Cell Line, Tumor | Signal Transduction - physiology | Enhancer Elements, Genetic - genetics | Real-Time Polymerase Chain Reaction | Oncology, Experimental | Physiological aspects | Genetic aspects | Research | T cells | Health aspects | Cancer | Index Medicus | Biological Sciences
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10. Full Text Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases
by Gusev, Alexander and Lee, Phil and Lee, S. Hong and Trynka, Gosia and Finucane, Hilary and Vilhjálmsson, Bjarni J and Xu, Han and Zang, Chongzhi and Ripke, Stephan and Bulik-Sullivan, Brendan and Stahl, Eli A and Stahl, Eli and Neale, Benjamin M and Neale, Benjamin M and Corvin, Aiden and Walters, James T.R and Farh, Kai-How and Holmans, Peter A and Collier, David A and Huang, Hailiang and Pers, Tune H and Agartz, Ingrid and Agerbo, Esben and Albus, Margot and Alexander, Madeline and Amin, Farooq and Bacanu, Silviu A and Begemann, Martin and Belliveau, Richard A and Bene, Judit and Bergen, Sarah and Bergen, Sarah E and Bevilacqua, Elizabeth and Bigdeli, Tim B and Black, Donald W and Børglum, Anders D and Bruggeman, Richard and Buccola, Nancy G and Buckner, Randy L and Byerley, William and Cahn, Wiepke and Cai, Guiqing and Campion, Dominique and Cantor, Rita M and Carr, Vaughan J and Carrera, Noa and Catts, Stanley V and Chambert, Kimberly D and Chambert, Kimberly and Chan, Raymond C.K and Chen, Ronald Y.L and Chen, Eric Y.H and Cheng, Wei and Cheung, Eric F.C and Chong, Siow Ann and Cloninger, C. Robert and Cohen, David and Cohen, Nadine and Cormican, Paul and Craddock, Nick and Crowley, James J and Curtis, David and Davidson, Michael and Davis, Kenneth L and Degenhardt, Franziska and Del Favero, Jurgen and DeLisi, Lynn E and Demontis, Ditte and Dikeos, Dimitris and Dinan, Timothy and Djurovic, Srdjan and Donohoe, Gary and Drapeau, Elodie and Duan, Jubao and Dudbridge, Frank and Durmishi, Naser and Eichhammer, Peter and Eriksson, Johan and Escott-Price, Valentina and Essioux, Laurent and Fanous, Ayman H and Farrell, Martilias S and Frank, Josef and Franke, Lude and Freedman, Robert and Freimer, Nelson B and Friedl, Marion and Friedman, Joseph I and Fromer, Menachem and Genovese, Giulio and Georgieva, Lyudmila and Gershon, Elliot S and Giegling, Ina and Giusti-Rodrguez, Paola and Godard, Stephanie and Goldstein, Jacqueline I and Golimbet, Vera and Gopal, Srihari and Gratten, Jacob and Grove, Jakob and ... and Psychiat Genomics Consortium and SWE-SCZ Consortium and Schizophrenia Working Group of the Psychiatric Genomics Consortium
The American Journal of Human Genetics, ISSN 0002-9297, 11/2014, Volume 95, Issue 5, pp. 535 - 552
Regulatory and coding variants are known to be enriched with associations identified by genome-wide association studies (GWASs) of complex disease, but their... 
PRIOR INFORMATION | GENETIC-VARIATION | GENOTYPE IMPUTATION | GENETICS & HEREDITY | DNA ELEMENTS | SNPS | SCHIZOPHRENIA | LARGE-SCALE | LOCI | EXPRESSION | GENOME-WIDE ASSOCIATION | Computer Simulation | Humans | Genetic Diseases, Inborn - genetics | Inheritance Patterns - genetics | Genetic Variation - genetics | Models, Genetic | Genome-Wide Association Study - methods | Open Reading Frames - genetics | Regulatory Elements, Transcriptional - genetics | Genetic research | Epigenetic inheritance | Research | Genetic regulation | Genotype & phenotype | Biological variation | Disease | Simulation | Genomics | Cells | Index Medicus
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